GEO series

Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [RNAseq]

GSE271129 Homo sapiens (human) DNA methylation 18 samples Submitted 2025/03/31 Platform GPL24676

At a glance

DNA methylation · human · 18 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 18 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Epigenetic mechanisms govern the transcriptional activity of lineage-specifying enhancers; but recent work challenges the dogma that both chromatin accessibility and DNA hypomethylation are prerequisites for transcription, highlighting a need to understand their coordinated dynamics. We established a highly-resolved timeline of DNA demethylation, chromatin accessibility, and transcription factor (TF) occupancy during early human cell differentiation.

Read the full summary ↓

We show >30,000 lineage-specifying enhancers undergo rapid and transient accessibility changes associated with distinct periods of TF expression. By contrast, enhancer DNA methylation changes are prolonged, unidirectional and delayed relative to chromatin dynamics, creating discordant epigenetic states. Using 6-base sequencing to detect methyl-intermediate, 5hmC, revealed that, for a subset of enhancers, TET-mediated, active demethylation begins prior to, and is maintained independently of, TF binding. In fact, machine learning models trained on 5-hydroxymethylation can predict of future chromatin states. Complete demethylation persists long after TF binding and accessibility have dissipated, suggesting that long-lasting hypomethylation of certain enhancers is a historical record of previous activity.

This dataset

Open GSE271129 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE271129_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1130021 and SRA study SRP517087. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 18 more — browse all 18 samples with per-sample file links →

Datasets on a similar topic

GSE271127 Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [ATACme] 18 samples shares demethylation, accessibility, substained, discordant, progenitor, chromatin, dynamics, enhancer
GSE256316 SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [ChIP-Seq] 121 samples shares accessibility, chromatin, enhancer
GSE285741 LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair ChIP-seq 32 samples shares demethylation, accessibility, chromatin
GSE256317 SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [ATAC-Seq] 32 samples shares accessibility, chromatin, enhancer
GSE329420 Endothelial exosomes remodel chromatin accessibility and superenhancer in cancer cells to promote liver metastatic colonization 26 samples shares accessibility, chromatin, enhancer
GSE277922 Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids 25 samples shares accessibility, chromatin, dynamics
GSE285742 LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair [ATAC-seq] 20 samples shares demethylation, accessibility, chromatin
GSE268580 Highly multiplexed single cell chromatin regulator and accessibility profiling elucidates chromatin dynamics in human B cell development and oncogenesis, and reveals an adverse prognostic gene expression signature in B lymphoblastic leukemias 15 samples shares accessibility, chromatin, dynamics

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